Bump nmdc-schema from 11.2.1 to 11.3.0 and sync transitive deps

[eecavanna]

On this branch, I bumped the nmdc-schema package dependency version from 11.2.1 to 11.3.0.

Details

I also documented a Docker command that makes it so make update-deps runs within a Docker container.

Related issue(s)

Fixes #873

Related subsystem(s)

• Runtime API (except the Minter)
• Minter
• Dagster
• Project documentation (in the docs directory)
• Translators (metadata ingest pipelines)
• MongoDB migrations
• Other

Testing

• I tested these changes (explain below)
• I did not test these changes

I will delegate the testing to the GHA workflows that process this PR.

Documentation

• I have not checked for relevant documentation yet (e.g. in the docs directory)
• I have updated all relevant documentation so it will remain accurate
• Other (explain below)

Maintainability

• Every Python function I defined includes a docstring (test functions are exempt from this)
• Every Python function parameter I introduced includes a type hint (e.g. study_id: str)
• All "to do" or "fix me" Python comments I added begin with either # TODO or # FIXME
• I used black to format all the Python files I created/modified
• The PR title is in the imperative mood (e.g. "Do X") and not the declarative mood (e.g. "Does X" or "Did X")

[eecavanna]

Note to reviewers: Once this PR has been approved by at least one person, you can proceed to merge it into main by clicking the "Merge pull request" button (which will be green at that time).